A Novel Single Nucleotide Polymorphism in Exon 4 of Insulin-Like Growth Factor-1 Associated with Production Traits in Bali Cattle

Abstract

ABSTRAKInsulin-like growth factor-1 (IGF-1) adalah salah satu kandidat gen dalam strategi seleksi menggunakan marka DNA (marker assisted selection). Strategi kandidat gen merupakan teknik biologi molekuler untuk mengidentifikasi lokus sifat kuantitatif secara langsung, dengan asumsi bahwa variasi genetik kandidat gen ini berasosiasi dengan sifat kuantitatif. Penelitian ini dirancang untuk mengidentifikasi adanya mutasi baru pada exon 4 yang dapat menimbulkan polimorfisme gen IGF-1 yang mempengaruhi sifat produksi pada sapi bali. Pencarian single nucleotide polymorphism (SNPs discovery) dilakukan menggunakan metode "direct sequencing", sedangkan variasi genetik kandidat gen ini diidentifikasi menggunakan teknik "polymerase chain reaction-restriction fragment length polymorphism" (PCR-RFLP). Hasil penelitian ini menunjukkan bahwa pada exon 4 gen IGF-1 ditemukan SNPs baru, yaitu mutasi transisi T/C, yang kemudian dapat identifikasi menggunakan enzim restriksi Rsa1. Polimorfisme genotipe IGF-1/Rsa1 memiliki pengaruh yang signifikan terhadap bobot lahir, bobot sapih, dan rata-rata pertambahan bobot badan harian sapi bali. Genotipe CC memiliki angka bobot lahir, bobot sapih, dan rata-rata pertambahan bobot badan harian berturut-turut: 15,64±1,83; 83,15±9,00; dan 0,439±0,07 yang lebih tinggi dibandingkan genotipe TT dan CT. Genotipe IGF-1/ Rsa1 dapat digunakan sebagai penciri genetik untuk seleksi bobot lahir, bobot sapih, dan pertambahan bobot badan harian.Kata kunci: gen, mutasi, restriksi, polimorfisme, marka, seleksi ABSTRACT Insulin-like growth factor-1 (IGF-1) is one of the gene candidates that can be used in selection strategy by using DNA markers (marker assisted selection). Gene candidate strategy is a molecular biology techniques to identify quantitative trait loci directly, with the assumption that genetic variation associated to quantitative trait variation. This study was designed to identify any new mutations in exon 4 that can cause the IGF-1 gene polymorphism and then affect the production traits on Bali cattle. Single nucleotide polymorphism (SNP) discovery was conducted by using the direct sequencing technique. Genetic variation of the genes candidate was identified by using PCR-RFLP technique. The results of this study indicate the presence of a new SNP in exon 4 of IGF-1 gene caused by the T/C transition, which can be identified using Rsa1 restriction enzyme. Genotypic polymorphism of IGF-1/Rsa1 has a significant influence on birth weight, weaning weight and average daily gain of Bali cattle. CC genotype had a birth weight rate, weaning weight and average daily gain of: 15.64±1.83; 83.15±9.00, and 0.439±0.07 respectively, higher than the TT and CT genotype. IGF-1/Rsa1 can be used as a genetic marker for selection of birth weight, weaning weight, and daily body weight gain.

Genetic polymorphisms of IGF1, GH, and OPN genes in crosses Peranakan Ongole cattle based on birth type in Central Java

“…Yurnalis et al (2017) from a study in local Pesisir cattle in West Sumatera reported frequencies of AA, AB, and BB genotypes were successively 0.0125, 0.0125, and 0.9750 and resulted frequencies of A and B alleles were 0.00625, and 0.99375 respectively. Genetic polymorphism of IGF-I gene was also reported from Bali cattle of which an SNP as a transition mutation T/C being identified by restriction enzyme RsaI at exon 4 with the frequency of C allele higher than that of T allele, namely 0.836 vs. 0.164 (Maskura et al 2012). Furtherly genotyping IGF1 by PCR -RFLP method using TaqI and MspI restriction enzymes and amplification-created restriction site (ACRS) one by SnaBI, TasI and TaqI restriction enzymes in Poland Cattle, Szewczuk (2016) reported frequencies of the most common alleles by 0.67 for T allele (IGF1|SnaBI), 0.85 for A allele (IGF1|TasI), 0.95 for C allele (IGF1R|TaqI), 0.84 for G allele (IGF1R|MspI) and 0.69 for G allele (IGF1R|TaqI).…”

Genotyping in the Insulin-like Growth Factor 1 (IGF1/SnaBI) gene of Pasundan cattle with PCR-RFLP method

“…The further study regarding to detect SNP along IGF1 gene is important for developing marker assisted selection (MAS) to improve productivity traits of Pasundan cattle in the future. Several studies reported that the polymorphism of bovine IGF1 gene were occured in exon 4 and had associated with production traits in Bali cattle (Maskur et al 2012). Mullen et al (2011) reported that polymorphisms of bovine IGF1 gene were occured in 5' UTR, intron and 3' UTR.…”

Exploring the relationship between polymorphisms of leptin and IGF-1 genes with milk yield in indicine and taurine crossbred cows

“…In another study, (Lynch et al , 2010) SNPs, IGFi1A-T, IGFi2C-T, IGFi3G-A, in IGF-1 were associated with milk production traits and BCS; and are in the agreement with our findings. Other studies reported that the polymorphism of bovine IGF-1 gene in exon 4 were associated with production traits in Bali cattle (Maskur et al ., 2012) but polymorphism in the intron 4 of IGF-1 gene was not associated with production traits in mixed population of Charolais and Beef master cattle (Reyna et al ., 2010).…”